The Barrett Group is looking for a new postdoc in statistical and computational genetics. Details about the position are after the fold; if you’re interested, contact Jeff directly.
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The Barrett group works on medical genomics research at the Wellcome Trust Sanger Institute. We are interested in how genomic variation affects risk for diseases, and in finding ways to apply that knowledge to improve health care. We analyze both genome-wide association studies and next-generation sequence data collected on thousands of individuals, develop statistical and computational methods for these analyses, and pursue the integration of genomics with medicine.
You can keep up to date with news and posts about our research by subscribing to our RSS feed.
On the weekend of 22nd of March, we went on our annual team retreat to Waterhouses, a village in the south of the Staffordshire Peak District. We set off from Oxford following a symposium at the Wellcome Trust Center of Human Genetics. Along the way we stopped in Lichfield to visit the famous Cathedral and the house of Erasmus Darwin (grandfather of Charles Darwin, www.erasmusdarwin.org). Surprisingly, Erasmus Darwin’s work hinted at the possibility of evolution, and although they had never met, Charles’ inspiration could have potentially come from his grandfather. We also had a nice meal in the Damn Fine Café, which had a selection of food and drink perfect for a cold winter’s afternoon.
We were really fortunate not to have lingered too long in Lichfield, as a large snowstorm rapidly descended upon the region. More »
One of the main research focuses of the Barrett group is to understand genetic associations with Inflammatory Bowel Disease (IBD), in particular with its two most common subtypes, Crohn’s disease and ulcerative colitis (UC).
Back in November 2012, in preparation for the ASHG meeting, I did a brief literature review on the development of IBD based on a number of selected publications. The motion chart below (created in R as used in the well-known Hans Rosling TED talk) shows an overview of the discovery of IBD disease loci since 2001, when three independent groups identified a CD risk gene on chromosome 16q12, NOD2, using linkage techniques.
Plot: IBD Motion Chart
R version 2.15.2 (2012-10-26) • googleVis-0.2.17 • Google Terms of Use • Data Policy
R version 2.15.2 (2012-10-26) • googleVis-0.2.17 • Google Terms of Use • Data Policy
Out today in Bioinformatics is an applications note describing our Olorin software. Olorin is an easy to use tool for filtering variants identified by high throughput family sequencing studies. Using Olorin, variants can be prioritized based on haplotype sharing across selected individuals in a pedigree as well as many other measures such as predicted functional consequence and population frequency.
The American Society of Human Genetics (ASHG, pronounced “A-shag”), annual meeting is a scientific, networking and socializing milestone every year. This year the meeting was 8 time zones away from the UK in San Francisco, CA. It was a busy year for our group, with 4 talks and a poster being presented, a variety of collaborators’ meetings to attend, a choice of hundreds of talks to listen to, and, of course, plenty of drinking to do.
Each member of the group who was there offers their thoughts after the break. It’s interesting to see that while we covered a wide variety of topics across the group, the most consistent message is that this year didn’t yield any major discoveries that will change the field. Instead, we all saw incremental progress in applying next-gen sequencing and similar technologies to many different problems. Perhaps this is simply a reflection of the nature of modern human genetics: a gradual improvement of our understanding, rather than a sudden revelation.
Out this week in Nature is the first big paper from the inflammatory bowel disease Immunochip project. The international project collected data from over 75 thousand individuals, and brought the total number of known IBD loci to a record-breaking 163. You can read more about the paper on the Sanger Institute website.
One interesting thing about the paper was how difficult it was to visualize the results. With one exception there were no single image that naturally fell out of any of the analyses, and we had to put quite a bit of work into displaying the messages of the paper in the figures. You can judge for yourself how much success we had, but I can say that up until the last few days before submission we still had images that everyone hated but couldn’t think what to replace them with. The last one to be replaced was the evocatively named “Smear-o-venn”, that we were all relieved to see the back of.
Congratulations to Luke on submitting the first PhD thesis from the group! He would’ve posted on the experience himself, but he’s enjoying some well earned rest at an undisclosed location.
Isabelle: About a month ago, I joined the Barrett-group at the Sanger institute. Coming from a molecular biology background and ending up in a team of computational biologists, statistical geneticists and bio-informaticians, it soon became clear that I was going to have to learn a whole new vocabulary: the ‘others’ love terms ending in *ash: bash, hash, slash (forward and backward!), dash…; and their day to day language includes things like grep (‘grepped’), awk, sed, syntax, R, perl, python, unix, linux (what is actually the difference between all these things??), … . Although I thought I was getting along very well before, manipulating datafiles in MS Excel and here and there using some command line programs (already making me feel like a computer wizard), it here turned out quickly that I was far from being a computer genius. I got lucky though, since one of my new colleagues appeared to be a ‘partner in crime’, also having a background in molecular biology, but having been introduced into the wonderful world of scripting and programming already years ago.
Iris: although I made the switch a while ago, until I started at Sanger I have always worked in a clinical setting so the wet lab was always just around the corner. In the Sanger introduction day there is a lot of attention placed on the campus desire to be as green as possible. More »
About a year ago I tried to regain control of my schedule, my work, my life by fully implementing Getting Things Done. Perhaps unsurprisingly I fell off the bandwagon pretty quickly. I think this is the experience of many people trying to change the way they organize their lives, and I’m planning a reboot soon. Nonetheless, many of the core GTD principles have been incubating in my mind and I’m trying to incorporate them into my day-to-day life even without the overarching organizational system.
One of the most profound of these concepts was the idea of redefining “productivity”. I think too often productivity is conflated with busyness; if we’re busy doing something then we must be being productive. In a great series of podcasts about life as a modern academic, however, MIT Physics Prof. Peter Fisher warns against activities which keep you busy without actually being productive — which raises the question, “What is productivity?”
[For the last two years, the Sanger Institute has been running a series of events looking at the relationship between society and personal genomics. This is a report on our most recent event, a debate on celebrity genomes between two campus faculty. In addition to the live debate and in-house questions, we also took comments on Twitter with the #CelebGenomes tag.]
In the second campus debate on “Society and the personal genome” Ewan Birney (proponent) and Paul Flicek (opponent) went head to head to debate the motion: “This House believes that celebrity genomes are a useful contribution to science and society”. The debate was well attended, with standing room only in the 150-seat lecture theatre. Prior to commencing the debate, Jeff (as Chair) took a poll of the audience, finding an even split among those who agreed (30%), disagreed (38%) and were undecided (32%). The same result was obtained using both high-tech interactive voting keypads and the more traditional method of estimating the decibels of a shouting crowd.
Opening arguments
Ewan opened by highlighting the two points of argument in this debate: 1) are celebrity genomes useful to science and 2) are they useful to society? He argued in response to the first question that famous genomes such as Desmond Tutu, James Watson and Craig Venter have already been used and widely cited in scientific research. To answer the second, he argued that for science to be useful for society, however, there needs to be a dialog between science and society. Society needs a narrative to understand the science, and celebrities are often where society turns for these stories. We need more people of every kind to talk about their genomes but the people that other people will notice are the celebrities.
In his opening argument, Paul made an important distinction between the genomes of “celebrity scientists” (James Watson, Craig Venter), and the genomes of popular celebrities (Simon Cowell, Ozzy Osbourne). The former may be well known in the scientific community, but if we are talking about “celebrity genomes”, we should really be talking about people who a significant proportion of the population know about. And the issue with these celebrities is that their genomes, and the insights they have into their genomes, are not more important than for any non-celebrity. He contrasted celebrity genomes with the example of Michael J. Fox’s Parkinson’s activism: Fox is a good celebrity advocate because of the unique insights that come from suffering from a condition that most people do not have, but everyone has a genome, so what makes celebrities more qualified to speak about genomics? Especially when we know celebrities are often terrible at communicating science to the public, as illustrated by an example of reality TV-star Nicole ‘Snooki’ Polizzi from the Jersey Shore who thinks the ocean is salty due to whale sperm.
Andrew Miller “Do A-listers have more A bases? #CelebGenomes”
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